Software | Research Software Directory

MOTrainer

Measurement Operator Trainer for data assimilation purposes.

Data assimilation
High performance computing
Machine learning
+ 2

("Jupyter Notebook")
(Python)
(Shell)
+ 1

7

2

NEWSGAC platform

Software for running the online platform of the NEWSGAC project for running explainable machine learning models on textual data

Explainable AI
Machine learning
Text analysis & natural language processing

(CSS)
(Dockerfile)
(HTML)
+ 4

3

2

ochre

A tool to clean up text generated by OCR using individual words as well as their context.

Machine learning
Text analysis & natural language processing

("Common Workflow Language")
(HTML)
("Jupyter Notebook")
+ 2

1

2

PathVisio

PathVisio is a free open-source software to curate biological pathway models.

bioinformatics
PathVisio
Systems Biology
+ 2

(Batchfile)
(CSS)
(HTML)
+ 4

9

2

PIDIMEHS library

Showcases a diachronic analysis of the Dutch Royal Library's newspaper archive.

Big data
Real time data analysis
Text analysis & natural language processing
+ 1

2

pyglotaran

A Python library for Global and Target Analysis of time-resolved spectroscopy data

biophysics
global analysis
glotaran
+ 3

(Nix)
(Python)

4

2

Ricgraph - Research in context graph

With Ricgraph (Research in context graph), you can create a graph from research information that is stored in various source systems. You can explore this graph and discover relations you were not aware of.

graph
graph database
research in context graph
+ 2

(CSS)
(Dockerfile)
(HTML)
+ 5

1

2

sfb-annotator

Annotate field books of natural history collections

Inter-operability & linked data

(CSS)
(Dockerfile)
(Java)
+ 4

3

2

ShiCo

A visualization that shows how the meaning we attach to a given concept shifts over time.

Text analysis & natural language processing
Visualization

(CSS)
(Dockerfile)
(HTML)
+ 3

1

2

swiftmhc

SwiftMHC is a deep learning algorithm for predicting pMHC structure and binding affinity at the same time.

deep learning
Protein-Protein Interaction
Transformer

("Jupyter Notebook")
(Mask)
(Python)
+ 1

3

2

tortellini

GitHub action to check whether any licensing issues exist for given software.

(JavaScript)
(TypeScript)

4

2

Pedestrian random walk in NetLogo (ch2.1)

A collection of methods for random walk in NetLogo, including various movement restrictions, biases, and algorithm alternatives.

4

1

Place them on the map

Multiple agent placement in specific geographical location. Set up an input number of agents (turtles) at an input location (cell or patch) in an grid holding the input spatial data (map).

5

1

Epidemic Network

Experimental environment for testing of large array of theoretical conditions for development epidemic event within various quantitative, spatial and connectedness (network structure) aspects.

2

1

Preferential Attachment Network

This NetLogo algorithm simulates network formation using preferential attachment. New nodes are more likely to connect to existing nodes with higher degrees, reflecting a "lottery" system where popular nodes attract more links.

1

Visualising GIS Rasters and Vector Data in NetLogo

This module provides a framework for importing and visualising GIS data in NetLogo. It supports continuous raster data visualised using colour gradients, binary and categorical raster data visualised using discrete colour assignments, and point-based vector data visualised as turtle agents.

1

AnisoVision

Data accompanying the publication: Characterization of the 3D-optical properties of van der Waals materials with deep learning based coherent Fourier scatterometry

anisotropic thin films
coherent Fourier scatterometry
deep learning metrology
+ 2

("Jupyter Notebook")
(Markdown)
(Other)

9

1

auction-tas

Truck Appointment Systems - Auction Based

Auction
competition
Scheduling
+ 2

("Jupyter Notebook")
(large-text-file)
(Markdown)
+ 2

1

Code and data belonging to the publication "Data-enabled Predictive Repetitive Control"

Data-driven control
Data-enabled Predictive Control
Fundamental Lemma
+ 2

(Markdown)
(Matlab)
(Other)

4

1

Code underlying the publication: "Video BagNet: short temporal receptive fields increase robustness in long-term action recognition"

3D-CNN
Action recognition
BagNet
+ 2

(Markdown)
(Other)
(Python)
+ 1

4

1

CounterfactualExplanations.jl

Software and data underlying the publication: Explaining Black-Box Models through Counterfactuals

Algorithmic Recourse
Counterfactual Explanations
explainable artificial intelligence
+ 1

(CSS)
(JavaScript)
(JSON)
+ 7

3

1

Data and code underlying the publication: Deep learning reveals key predictor of thermal conductivity of covalent organic frameworks

Covalent organic frameworks
deep learning
Thermal conductivity
+ 1

5

1

Dataset-NonDimensionalisationQMOM

Data to reproduce the paper: "Non-dimensionalization of quadrature method of moments for wet granulation"

10th granulation conference Sheffield
Buckingham Theorem
non-dimensionalization
+ 3

(Markdown)
(Matlab)
(Other)
+ 1

3

1

det2d-read

Python package to read 2D human poses from json files

2D pose detection
Data loading
Multiprocessing
+ 1

(JSON)
(Markdown)
(Other)
+ 2

1

Effects of PLU Polling Interval

The codes associated with the publication: The Effects of PLU Polling Interval on the Reconstructed OD Matrix: A Dutch Case Study Using a Data-Driven Method

Bayesian
GSM
OD matrix
+ 2

("Jupyter Notebook")
(Markdown)
(Other)

3

1

Hodge-Edge-GP

Code underlying: Hodge-Compositional Edge Gaussian Processes

edge space
forex
Gaussian process
+ 2

(JSON)
("Jupyter Notebook")
(Markdown)
+ 3

1

IntervalMDPAbstractions.jl_ReproducibilityPackage

Data and code underlying the publication: Scalable control synthesis for stochastic systems via structural IMDP abstractions

embedded systems
Markov processes
Stochastic control and optimization

(C)
(C++)
(HTML)
+ 10

3

1

longterm_datasets

Code underlying the publication: "Are current long-term video understanding datasets long-term?"

computer vision
deep learning
Long-term action recognition

(HTML)
(Markdown)
(Other)
+ 2

3

1

LOV3D

LOV3D: A Spectral Method to Compute the Tides of Laterally Heterogenous Bodies (v2.3)

Natural Satellites
Planetary Sciences
Tides

(CSS)
(HTML)
(Markdown)
+ 2

3

1

mason_constitutive_model

MASON (Masonry Advanced Softening cONtact) source code

cyclicity
distinct element method
explicit integration scheme
+ 3

(C)
(C++)
(Markdown)
+ 1

1

mean-field-quantum-networks

Code underlying the publication: Service-the-Longest-Queue Among d Choices Policy for Quantum Entanglement Switching

entanglement generation switch
load-balancing.
mean-field analysis
+ 1

(JSON)
(Julia)
(Markdown)
+ 2

1

NetLogo model: "Urbanism and Geographic Crises: A Micro-Simulation Lens on Beirut"

agent-based simulation
Beirut
econometrics
+ 3

2

1

Online COP heuristic learning code: "Online Learning of Variable Ordering Heuristics for Constraint Optimisation Problems"

constraint optimisation problem
Gecode
Machine learning
+ 3

2

1

P1-data-combination-code

Code to paper "Changing Sea Level, Changing Shorelines: Integration of Remote Sensing Observations at the Terschelling Barrier Island"

coastline
Remote sensing
sea level
+ 1

("Jupyter Notebook")
(large-text-file)
(Markdown)
+ 1

3

1

patient-interaction-detection

Python code to detect interaction of medical personnel with the operating table from surveillance videos

2D human poses
Action recognition
Operating table interaction
+ 3

(JSON)
(large-text-file)
(Markdown)
+ 2

1

ProbabilisticValidation

Source code underlying the publication: Privacy-Preserving Data Aggregation with Probabilistic Range Validation

privacy-preserving summation
range validation
secure multi-party computation
+ 1

(Markdown)
(Matlab)

2

1

Software accompanying the publication: Surrogate DC Microgrid Models for Optimization of Charging Electric Vehicles under Partial Observability

DC microgrid
Electric vehicles (EV),
Optimization Algorithms

3

1

Software underlying the article: Modelling the cross-sectional dynamics of tidal sandbanks in sediment-scarce conditions

Asymmetry
Coastal Engineering
Equilibrium shape
+ 12

3

1

Soil suitability maps for agriculture for the province Noord-Brabant (Netherlands) created with WaterVissionAgriculture and scripts to generate input data and to run the model WWL-tabel

Agriculture
crop production
soil suitability
+ 2

2

1

Source code for: Assessing the Validity of a Calcifying Oral Biofilm Model as a Suitable Proxy for Dental Calculus

dental calculus
Fourier-transform infrared spectroscopy (FTIR)
metagenomics
+ 2

5

1

supervised-learning-pwa-mpc

Software underlying the publication: Learning-based model predictive control for piecewise affine systems with feasibility guarantees

Feasibility
Hybrid Systems
Machine learning
+ 1

(Markdown)
(Matlab)
(Other)
+ 1

1

swinging-kite

Swinging Motion of a Kite with Suspended Control Unit Flying Turning Manoeuvres (Code)

Airborne Wind Energy (AWE)
Flight data analysis
Kite power
+ 2

(Markdown)
(Other)
(Python)
+ 1

1

SWMM_GNN_Component_Evaluation_and_Transferability_Analysis

Code for paper "Evaluation of Graph Neural Networks for Urban Drainage Metamodeling: Key Components and Transferability Analysis"

Graph Neural Network
Hyperparameter Tuning
Stormwater management model (SWMM)
+ 3

("Jupyter Notebook")
(Markdown)
(Other)
+ 2

4

1

Analizo

Analizo is a free, multi-language, extensible source code analysis. It supports the extraction and calculation of a fair number of source code metrics, generation of dependency graphs, and software evolution analysis.

Software Evolution
Source Code Metrics
Static Analysis

(C)
(C#)
(C++)
+ 7

2

1

anonymoUUs

Python package to replace identifiable strings in multiple files and folders at once

de-identification
python
text

("Jupyter Notebook")
(Python)

3

1

Baklava

Deploys a Kubernetes cluster and big data services on the cloud.

Big data
High performance computing
Optimized data handling

(Dockerfile)
(HCL)
(Python)
+ 2

1

BenchmarkRecovery

This project simulates Landsat data and evaluates the performance of recovery indicators with respect to data and disturbance characteristics.

(R)

2

1

BestieTemplate.jl

BestieTemplate.jl is a template focused on best practices for package development in Julia.

best practices
julia
template

(Julia)

9

1